Sequence
atgc intronic sequence ATGC exonic sequencegttaggagtaatggattttaatgttaatttttttaaaaaaatcatcacatagtttagtactttgtttattttgatgaactttgcttctttttttttcttttggggttcatggattttgttagGCATAGATGGACTGGAAGATATGAGGCCCATTTGTGGGATAATAGTTGCAGAAAGGAAGGGCAAACAAGGAAAGGAAGGCAAG
Basic information
species | Glycine max |
transcript | GLYMA16G00950.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G00950.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g07940.1 (Oryza sativa), 3'ss of exon 2
gttaggagtaatggattttaatgttaatttttttaaaaaaatcatcacatagtttagtactttgtttattttgatgaactttgcttctttttttttcttttggggttcatggattttgttagGCATAGATGGACTGGAAGATATGAGGCCCATTTGTGGGATAATAGTTGCAGAAAGGAAGGGCAAACAAGGAAAGGAAGGCAAG
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------------------------------------gttggtgacgacattgct-gcttctccattgcttccggcgtgtctcactgatccatgtctacgt----gctcatcatttttttcagACATAGATGGACTGGAAGATACGAGGCTCACTTGTGGGACAACACTTGCAGGAAGGAAGGCCAGACCAGGAAAGGAAGGCAAG
upper sequence: GLYMA16G00950.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0002g01370.t01 (Vitis vinifera), 3'ss of exon 3
gttaggagtaatggattttaatgttaatttttttaaaaaaatcatcacatagtttagtactttgtttattttgatgaactttgcttctttttttttcttttggggttcatggattttgtt--agGCATAGATGGACTGGAAGATATGAGGCCCATTTGTGGGATAATAGTTGCAGAAAGGAAGGGCAAACAAGGAAAGGAAGGCAAG
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-----------------------------gtattgaaagaa-----acaaattttaattcttttcttttctt----ttctttgaagagaaaattttgatgggtgggtgatgaaatttgttttagGCACAGATGGACTGGAAGATATGAAGCCCATTTGTGGGACAACAGTTGCAGAAAAGAAGGACAAACAAGGAAAGGAAGGCAAG
upper sequence: GLYMA16G00950.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S131_131V6.1 (Physcomitrella patens), 3'ss of exon 2
gttaggagtaatggattttaatgttaatttttttaaaaaaatcatcacatagtttagtactttgtt-tattttgatgaactttgcttctttttttttcttttggggttcatggattttgttagGCATAGATGGACTGGAAGATATGAGGCCCATTTGTGGGATAATAGTTGCAGAAAGGAAGGGCAAACAAGGAAAGGAAGGCAAG
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-----gggtg-tagagctgaatttaggcttg---gcgaaggtcg--aagtggttgagggtcatgtcctggtctgaggatgttggggggtgtattgtgtgtttga-----------tttgt-agGCATCGTTGGACTGGACGGTACGAGGCACATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG
upper sequence: GLYMA16G00950.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 1
gttaggagtaatggattttaatgttaatttttttaaaaaaatcatcacatagtttagtactttgtttattttgatgaactttgcttctttttttttcttttggggttcatggattttgttagGCATAGATGGACTGGAAGATATGAGGCCCATTTGTGGGATAATAGTTGCAGAAAGGAAGGGCAAACAAGGAAAGGAAGGCAAG
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----ggcgcag-agagctaaattttagcctg---gcgaaggtcg--aagttgttgagggtcatatcctggtctgaggatgttggggggtgtattgtgtgttga-----------tttgt-agGCATCGTTGGACTGGACGGTACGAGGCTCATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttgatgaactttgcttctttttttttcttttggggttcatggattttgttagGCATAGATGGACTGGAAGATATGAGGCCCATTTGTGGGATAATAGTTGCAGAAAGGAAGGGCAAACAAGGAAAGGAAGGCAAG
ttttgat putative branch site (score: 4)
ttttgtt putative PPT
ttctttttttttcttt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaggagtaatggattttaatgttaatttttttaaaaaaatcatcacatagtttagtactttgtttattttgatgaactttgcttctttttttttcttttggggttcatggattttgttagGCATAGATGGACTGGAAGATATGAGGCCCATTTGTGGGATAATAGTTGCAGAAAGGAAGGGCAAACAAGGAAAGGAAGGCAAG
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